scholarly journals Correlating Bayesian date estimates with climatic events and domestication using a bovine case study

2008 ◽  
Vol 4 (4) ◽  
pp. 370-374 ◽  
Author(s):  
Simon Y.W Ho ◽  
Greger Larson ◽  
Ceiridwen J Edwards ◽  
Tim H Heupink ◽  
Kay E Lakin ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Divergence Times ◽  
Zebu Cattle ◽  
Important Species ◽  
Radiocarbon Dates ◽  
Bayesian Phylogenetic Analysis ◽  
D Loop ◽  
Major Haplogroups ◽  
Age Estimates

The tribe Bovini contains a number of commercially and culturally important species, such as cattle. Understanding their evolutionary time scale is important for distinguishing between post-glacial and domestication-associated population expansions, but estimates of bovine divergence times have been hindered by a lack of reliable calibration points. We present a Bayesian phylogenetic analysis of 481 mitochondrial D-loop sequences, including 228 radiocarbon-dated ancient DNA sequences, using a multi-demographic coalescent model. By employing the radiocarbon dates as internal calibrations, we co-estimate the bovine phylogeny and divergence times in a relaxed-clock framework. The analysis yields evidence for significant population expansions in both taurine and zebu cattle, European aurochs and yak clades. The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison – Bos divergence.

scholarly journals Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1645-1656 ◽  
Author(s):  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Dna Sequences ◽  
Gene Tree ◽  
Species Tree ◽  
Bayes Estimation ◽  
Ancestral Population ◽  
Divergence Times ◽  
Gene Trees ◽  
Species Divergence ◽  
Multiple Loci ◽  
Population Sizes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

Points in Time: Direct Radiocarbon Dates on Great Basin Projectile Points

2013 ◽  
Vol 78 (3) ◽  
pp. 580-594 ◽  
Author(s):  
Geoffrey M. Smith ◽  
Pat Barker ◽  
Eugene M. Hattori ◽  
Anan Raymond ◽  
Ted Goebel
Keyword(s):  
Great Basin ◽  
Archaeological Sites ◽  
Projectile Point ◽  
Radiocarbon Dates ◽  
Projectile Points ◽  
Primary Means ◽  
Point Types ◽  
Cross Dating ◽  
Age Estimates

AbstractTypological cross-dating is the primary means by which archaeological sites are placed into chronological frameworks. This approach relies on the assumption that artifacts at undated sites—usually projectile points—are coeval with similar artifacts found at Other, dated sites. While typological cross-dating is necessary in regions dominated by open-air lithic scatters, the approach can be problematic when undated and dated sites are separated by significant distances. Here, we present radiocarbon dates on projectile points with organic hafting material still attached or found within organic storage bags. Our results provide unequivocal ages for various morphological projectile point types at several Great Basin locales and should be useful to researchers seeking local age estimates for those point types, which often involves relying on chronological data from more distant sites. The results also highlight potential issues with uncritically applying typological cross-dating using typologies based on metric attributes, and in two cases, suggest the need to revise the age ranges for certain point styles in the western Great Basin.

scholarly journals Dating ancient human samples using the recombination clock

2015 ◽  
Author(s):  
Priya Moorjani ◽  
Sriram Sankararaman ◽  
Qiaomei Fu ◽  
Molly Przeworski ◽  
Nick J Patterson ◽  
...  
Keyword(s):  
Best Practice ◽  
Radiocarbon Dates ◽  
Genetic Method ◽  
Human Samples ◽  
Shared History ◽  
Complementary Approach ◽  
Neanderthal Admixture ◽  
History Of ◽  
The Difference ◽  
Age Estimates

The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these is the reliable estimation of the age of ancient specimens. The current best practice is radiocarbon dating, which relies on characterizing the decay of radioactive carbon isotope (14C), and is applicable for dating up to 50,000-year-old samples. Here, we introduce a new genetic method that uses recombination clock for dating. The key idea is that an ancient genome has evolved less than the genomes of extant individuals. Thus, given a molecular clock provided by the steady accumulation of recombination events, one can infer the age of the ancient genome based on the number of missing years of evolution. To implement this idea, we take advantage of the shared history of Neanderthal gene flow into non-Africans that occurred around 50,000 years ago. Using the Neanderthal ancestry decay patterns, we estimate the Neanderthal admixture time for both ancient and extant samples. The difference in these admixture dates then provides an estimate of the age of the ancient genome. We show that our method provides reliable results in simulations. We apply our method to date five ancient Eurasian genomes with radiocarbon dates ranging between 12,000 to 45,000 years and recover consistent age estimates. Our method provides a complementary approach for dating ancient human samples and is applicable to ancient non-African genomes with Neanderthal ancestry. Extensions of this methodology that use older shared events may be able to date ancient genomes that fall beyond the radiocarbon frontier.

scholarly journals Dispersals as demographic processes: testing and describing the spread of the Neolithic in the Balkans

2020 ◽  
Vol 376 (1816) ◽  
pp. 20200231 ◽  
Author(s):  
Marc Vander Linden ◽  
Fabio Silva
Keyword(s):  
Food Production ◽  
Population History ◽  
Early Neolithic ◽  
Theme Issue ◽  
Radiocarbon Dates ◽  
The Balkans ◽  
Demographic Processes ◽  
South Eastern Europe ◽  
Density Dependent Dispersal

Although population history and dispersal are back at the forefront of the archaeological agenda, they are often studied in relative isolation. This contribution aims at combining both dimensions, as population dispersal is, by definition, a demographic process. Using a case study drawn from the Early Neolithic of South-Eastern Europe, we use radiocarbon dates to jointly investigate changes in speed and population size linked to the new food production economy and demonstrate that the spread of farming in this region corresponds to a density-dependent dispersal process. The implications of this characterization are evaluated in the discussion. This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.

Comments on Radiocarbon Dates from Mexico

1951 ◽  
Vol 8 ◽  
pp. 33-36 ◽  
Author(s):  
Helmut de Terra
Keyword(s):  
Glacial Lake ◽  
Radiocarbon Dates ◽  
Early Archaic ◽  
Basin Of Mexico ◽  
Monte Alban ◽  
Time Sequences ◽  
Age Estimates

In the Summer of 1949, I was asked to 1 cooperate in securing appropriate samples from important Mexican sites. These, I suggested, should be selected with a view of obtaining new data on three significant problems: early man and associated geologic formations, the Archaic cultures, and the monumental civilizations of Teotihuacan and Monte Alban. This choice was dictated by the prevailing chronologic uncertainties of prehistoric cultures in Mexico and by my previous geologic approaches to time sequences in the Basin of Mexico. Computations from glacial, lake and erosion phenomena had suggested that previous age estimates, notably those presented by Vaillant (1944) and other archaeologists, had been unduly conservative. This was especially evident in the case of the basic pottery levels, known as the early Archaic or early Middle cultures, then assumed to have existed about 2100 to 1600 years ago.

Are polymorphic species of Uropodina (Acari: Mesostigmata) more successful evolutionarily?—A case study of closely related species from the genus Oodinychus Berlese, 1917 based on DNA sequences

2019 ◽  
Vol 24 (5) ◽  
pp. 866
Author(s):  
Jerzy Błoszyk ◽  
Katarzyna Buczkowska ◽  
Anna Maria Bobowicz ◽  
Alina Bączkiewicz ◽  
Zbigniew Adamski ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Related Species ◽  
Habitat Preferences ◽  
Abundant Species ◽  
Systematic Position ◽  
Genetic Differences ◽  
Similar Species ◽  
Closely Related Species ◽  
Wide Range

The study presented in this research paper is the first taxonomic investigation focusing on Uropodina (Acari: Mesostigmata) mites with a brief discussion of the genetic differences of two very closely related species from the genus Oodinychus Berlese, 1917, i.e. O. ovalis (C.L. Koch, 1839) and O. karawaiewi (Berlese, 1903). These two morphologically similar species are quite common and they have a wide range of occurrence in Europe. They also live in almost the same types of habitat. However, O. ovalis usually exhibits higher abundance and frequency of occurrence. The major aim of the study was to carry out a comparative analysis of the systematic position, morphological and biological differences, as well as habitat preferences and distribution of O. ovalis and O. karawaiewi. The next aim was to ascertain whether the differences in number and frequency of these species may stem from the genetic differences at the molecular level (16S rDNA and COI). The study shows that O. ovalis, which is a more abundant species than O. karawaiewi, turned out to be genetically more polymorphic.

Advances in visualizing transcription factor-DNA interactions

Genome ◽  
2020 ◽  
Author(s):  
Rachel M. Price ◽  
Marek A Budzynski ◽  
Shivani Kundra ◽  
Sheila S. Teves
Keyword(s):  
Molecular Biology ◽  
Dna Sequences ◽  
Imaging Techniques ◽  
Specific Interaction ◽  
Dna Interactions ◽  
Dynamic Information ◽  
Transcription Process ◽  
Target Dna ◽  
Biology Research

At the heart of the transcription process is the specific interaction between transcription factors (TFs) and their target DNA sequences. Decades of molecular biology research have led to unprecedented insights into how TFs access the genome to regulate transcription. In the last 20 years, advances in microscopy have enabled scientists to add imaging as a powerful tool in probing two specific aspects of TF-DNA interactions: structure and dynamics. In this review, we examine how applications of diverse imaging technologies can provide structural and dynamic information that complements insights gained from molecular biology assays. As a case study, we discuss how applications of advanced imaging techniques have reshaped our understanding of TF behavior across the cell cycle, leading to a rethinking in the field of mitotic bookmarking.

scholarly journals Radiocarbon Dates and the Earliest Colonization of East Polynesia: More than a Case Study

Radiocarbon ◽  
2009 ◽  
Vol 51 (2) ◽  
pp. 681-693 ◽  
Author(s):  
Philippe Della Casa
Keyword(s):  
Vegetation History ◽  
French Polynesia ◽  
Easter Island ◽  
Sample Material ◽  
Ongoing Debate ◽  
Radiocarbon Dates ◽  
Almost All ◽  
Early Human ◽  
Archaeological Excavations

Over the last 30 yr, there has been an ongoing debate on the dates and modes of the earliest colonization of East Polynesia, namely the Cook Islands, the 5 archipelagos of French Polynesia, the Hawai'i Islands, Easter Island, and New Zealand. At least 3 alternative models were proposed by Sinoto, Anderson, Kirch, and Conte, but interestingly all these models basically relied on the same set of roughly 200 radiocarbon dates on various organic materials from archaeological excavations as far back as the 1950s. Some of the models differed by 500–1000 yr—for a proposed initial colonization around the turn of the BC/AD eras, if not considerably later. By comparing the different approaches to this chronological issue, it becomes evident that almost all known problems in dealing with 14C dates from archaeological excavations are involved: stratigraphy and exact location of samples, sample material and quality, inbuilt ages and reservoir effects, lab errors in ancient dates, etc. More recently, research into landscape and vegetation history has produced alternative 14C dating for early human impact, adding to the confusion about the initial stages of island colonization, while archaeological 14C dates, becoming increasingly “young” as compared to former investigations, now advocate a rapid and late (post-AD 900) colonization of the archipelagos. As it appears, the Polynesian case is more than just another case study, it's a lesson on 14C-based archaeological chronology. The present paper does not pretend to solve the problems of early Polynesian colonization, but intends to contribute to the debate on how 14C specialists and archaeologists might cooperate in the future.

Evaluating the Old Wood Problem in a Temperate Climate: A Fort Ancient Case Study

2014 ◽  
Vol 79 (04) ◽  
pp. 763-775 ◽  
Author(s):  
Robert A. Cook ◽  
Aaron R. Comstock
Keyword(s):  
North America ◽  
American Southwest ◽  
Wood Charcoal ◽  
Arid Climate ◽  
Temperate Climate ◽  
Radiocarbon Dates ◽  
Eastern Woodlands ◽  
Fort Ancient

Abstract Schiffer (1986) first identified the old wood problem for wood charcoal-based dates from archaeological contexts in the American Southwest. The potential for dates to be skewed toward excessively old calendar ages in this region has recently generated reticence in part of the archaeological community towards including wood charcoal dates in general. Some scholars have even begun to cleanse the radiocarbon databases of regions throughout North America, partly with this presumed limitation in mind. However, the issues that contribute to the old wood problem have not been closely examined outside the arid climate of the American Southwest, resulting in some studies excluding hundreds of radiocarbon dates. The present study fills that void by examining the radiocarbon record from four well-dated Fort Ancient sites in southwestern Ohio and southeastern Indiana. Specifically, we test whether or not there are significant differences between wood charcoal and non-wood charcoal assays. Our findings suggest that wood charcoal dates should not be excluded. We explore reasons for this difference in the Eastern Woodlands and propose an ideal dating regime.

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